Publications: (first or co-first author)


2009

Jiang, C and Pugh, BF (2009) Nucleosome positioning and gene regulation: advances through genomics.  Nature Reviews Genetics,  2009 Mar;10(3):161-72 Cover story

Jiang, C and Pugh, BF (2009) A compiled and systematic reference map of nucleosome positions across the Saccharomyces genome.  Genome Biology,  2009;10:R109 


2008

Mavrich, TN*, Jiang, CZ* (Co-first author), Ioshikhes, IP, Li, X, Venters, BJ, Zanton, SJ, Tomsho, LP, Qi, J, Glaser, RL, Schuster, SC, Gilmour, DS, Albert, I, Pugh, BF. (2008) Nucleosome organization in the Drosophila genome.  Nature,  2008 May 15;453(7193):358-62 Article


2007

Jiang, C*, Han, L*, Su, B, Li, WH and Zhao, Z (2007) Features and Trend of Loss of Promoter-Associated CpG Islands in the Human and Mouse Genomes.  Mol Biol Evol.,  2007 Sep;24(9):1991-2000

Jiang, C, Xuan, Z, Zhao, F, and Zhang, MQ (2007) TRED: a Transcriptional Regulatory Element Database, new entries and other development.  Nucleic Acids Res.,  2007 Jan;35:D137-D140


2006

Jiang, C and Zhao, Z (2006) Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome  BMC Genomics,  2006 Dec 13;7(1):316

Jiang, C and Zhao, Z (2006) Mutational spectrum in the recent human genome inferred by single nucleotide polymorphisms.  Genomics,  2006 Nov;88(5):527-34


2004

Jiang, C, Gu, X, and Peterson, T (2004) Identification of conserved gene structures and carboxy-terminal motifs in the Myb gene family of Arabidopsis and Oryza sativa L. ssp. indica.  Genome Biology,  2004;5(7):R46

Jiang, C, Gu, J, Chopra , S, Gu, X#, and Peterson, T# (2004) Ordered Origin of the Typical Two- and Three-Repeat Myb Genes.  Gene,  2004 Feb 4;326:13-22


1998

江赐忠, 宋文芹, 李秀兰, 陈瑞阳 (1998) 黑麦1R染色体的微切微克隆研究.  植物学报,  1998;40(11):988-993



Publications: (# corresponding or co-corresponding author)


2017

Du Y, Liu Z, Cao X, Chen X, Chen Z, Zhang X, Zhang X#, Jiang C#. (2017) Nucleosome eviction along with H3K9ac deposition enhances Sox2 binding during human neuroectodermal commitment.  Cell Death Differ,  2017 Jun;24(6): 1121-1131

Ye Y*, Li M*, Gu L, Chen X, Shi J, Zhang X#, Jiang C#. (2017) Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos.  Cell Death Differ,  2017 Mar;24(3):409-420


2016

Ye Y, Gu L, Chen X, Shi J, Zhang X#, Jiang C#. (2016) Chromatin remodeling during the in vivo glial differentiation in early Drosophila embryos.  Sci Rep. ,  2016 Sep 16;6:33422

Shi J*, He J*, Lin J, Sun X, Sun F#, Ou C#, Jiang C#. (2016) Distinct response of the hepatic transcriptome to Aflatoxin B1 induced hepatocellular carcinogenesis and resistance in rats.  Sci Rep. ,  2016 Aug 22;6:31898

Li D*, Shi J*, Du Y, Chen K, Liu Z, Li B, Li J, Tao F, Gu H, Jiang C#, Fang J#. (2016) Profiling Analysis of Histone Modifications and Gene Expression in Lewis Lung Carcinoma Murine Cells Resistant to Anti-VEGF Treatment.  PLoS One,  2016 Jun 30;11(6):e0158214

Chen J*, Chen X*, Li M*, Liu X, Gao Y, Kou X, Zhao Y, Zheng W, Zhang X, Huo Y, Chen C, Wu Y, Wang H, Jiang C#, Gao S#.  Cell Rep. ,  2016 Feb 16;14(6):1540-54


2015

Shen J*, Jia W*, Yu Y, Chen J, Cao X, Du Y, Zhang X, Zhu S, Chen W, Xi J, Wei T, Wang G, Yuan D, Duan T, Jiang C, Jiang C#, Kang J#. (2015) Pwp1 is required for the differentiation potential of mouse embryonic stem cells through regulating Stat3 signaling.  Stem Cells,  2015 Mar;33(3):661-73


2014

Tao Y*, Zheng W*, Jiang Y*, Ding G*, Hou X, Tang Y, Li Y, Gao S, Chang G, Zhang X, Liu W, Kou X, Wang H, Jiang C#, Gao S#. (2014) Nucleosome organizations in induced pluripotent stem cells reprogrammed from somatic cells belonging to three different germ layers.  BMC Biol.,  2014 Dec 21;12(1):109

Shi J*, Zheng M*, Ye Y, Li M, Chen X, Hu X, Sun J, Zhang X#, Jiang C#. (2014) Drosophila Brahma complex remodels nucleosome organizations in multiple aspects.  Nucleic Acids Res.,  2014 Sep;42(15):9730-9

Yin R*, Gu L*, Li M, Jiang C#, Cao T#, Zhang X#. (2014) Gene Expression Profiling Analysis of Bisphenol A-induced Perturbation in Biological Processes in ER-negative HEK 293 Cells.  PLoS One.,  2014 Jun 5;9(6):e98635

Li M, Liu Z, Gu L, Yin R, Li H, Zhang X, Cao T#, Jiang C#. (2014) Toxic effects of decabromodiphenyl ether (BDE-209) on human embryonic kidney cells.  Front Genet.,  2014 May 6;5:118

Lin J, Chen G, Gu L, Shen Y, Zheng M, Zheng W, Hu X, Zhang X, Qiu Y, Liu X#, Jiang C#. (2014) Phylogenetic affinity of tree shrews to Glires is attributed to fast evolution rate.  Mol. Phylogenet. Evol.,  2014 Feb;71:193-200


2013

Chen G*, Shi X*, Sun C, Li M, Zhou Q, Zhang C, Huang J, Qiu Y, Wen X, Zhang Y, Zhang Y, Yang S, Lu L, Zhang J, Yuan Q, Lu J, Xu G, Xue Y, Jin Z, Jiang C#, Ying M#, Liu X#. (2013) VEGF-mediated proliferation of human adipose tissue-derived stem cells.  PLoS One,  2013 Oct 3;8(10):e73673

Shi J*, Hu J*, Zhou Q, Du Y, Jiang C#. (2013) PEpiD: a Prostate Epigenetic Database in mammals.  PLoS One,  2013 May 16;8(5):e64289

Tang Y*, Dong S*, Cao X, Zhou Q, Ding G, Jiang C#. (2013) H2A.Z Nucleosome Positioning Has No Impact on Genetic Variation in Drosophila Genome.  PLoS One,  2013;8(3):e58295

Zhang X*#, Shen Y*, Ding G, Tian Y, Liu Z, Li B, Wang Y, Jiang C#. (2013) TFPP: An SVM-Based Tool for Recognizing Flagellar Proteins in Trypanosoma brucei.  PLoS One,  2013;8(1):e54032



Publications: (co-authorship)


2017

Chen K, Li D, Li H, Li B, Li J, Huang L, Li R, Xu X, Jiang L, Jiang C, Gu H, Fang J. (2017) Genetic analysis of heterogeneous sub-clones in recombinant Chinese hamster ovary cells.  Appl Microbiol Biotechnol,  2017 May 24. doi: 10.1007/s00253-017-8331-4. [Epub ahead of print]


2016

Wo D*, Peng J*, Ren DN*, Qiu L*, Chen J, Zhu Y, Yan Y, Yan H, Wu J, Ma E, Zhong TP, Chen Y, Liu Z, Liu S, Ao L, Liu Z, Jiang C, Peng J, Zou Y#, Qian Q#, Zhu W#. (2016) Opposing Roles of Wnt Inhibitors IGFBP-4 and Dkk1 in Cardiac Ischemia by Differential Targeting of LRP5/6 and β-catenin.  Circulation,  2016 Dec 13;134(24):1991-2007

Jin J*, Liu J*, Chen C, Liu Z, Jiang C, Chu H, Pan W, Wang X, Zhang L, Li B, Jiang C, Ge X, Xie X#, Wang P#. (2016) The deubiquitinase USP21 maintains the stemness of mouse embryonic stem cells via stabilization of Nanog.  Nat Commun,  2016 Nov 25;7:13594

Chi L*, Fan B*, Zhang K, Du Y, Liu Z, Fang Y, Chen Z, Ren X, Xu X, Jiang C, Li S, Ma L, Gao L#, Liu L#, Zhang X#. (2016) Targeted Differentiation of Regional Ventral Neuroprogenitors and Related Neuronal Subtypes from Human Pluripotent Stem Cells.  Stem Cell Reports,  2016 Nov 8;7(5):941-954

Lu P*, Chen X*, Feng Y*, Zeng Q, Jiang C, Zhu X#, Fan G#, Xue Z#. (2016) Integrated transcriptome analysis of human iPS cells derived from a fragile X syndrome patient during neuronal differentiation.  Sci China Life Sci.,  2016 Nov;59(11):1093-1105

Gao H*#, Chakraborty G*, Zhang Z, Akalay I, Gadiya M, Gao Y, Sinha S, Hu J, Jiang C, Akram M, Brogi E, Leitinger B, Giancotti FG#. (2016) Multi-organ Site Metastatic Reactivation Mediated by Non-canonical Discoidin Domain Receptor 1 Signaling.  Cell,  2016 Jun 30;166(1):47-62

Zhang S, Guo X, Chen C, Chen Y, Li J, Sun Y, Wu C, Yang Y, Jiang C, Li W#, Xue L#. (2016) dFoxO promotes Wingless signaling in Drosophila.  Sci Rep. ,  2016 Mar 3;6:22348

Liu L, Liu X, Ren X, Tian Y, Chen Z, Xu X, Du Y, Jiang C, Fang Y, Liu Z, Fan B, Zhang Q, Jin G, Yang X, Zhang X. (2016) Smad2 and Smad3 have differential sensitivity in relaying TGFβ signaling and inversely regulate early lineage specification.  Sci Rep. ,  2016 Feb 24;6:21602

Tee AE, Liu B, Song R, Li J, Pasquier E, Cheung BB, Jiang C, Marshall GM, Haber M, Norris MD, Fletcher JI, Dinger ME, Liu T. (2016) The long noncoding RNA MALAT1 promotes tumor-driven angiogenesis by up-regulating pro-angiogenic gene expression.  Oncotarget,  2016 Feb 23;7(8):8663-75

Li H, Chen K, Wang Z, Li D, Lin J, Yu C, Yu F, Wang X, Huang L, Jiang C, Gu H, Fang J. (2016) Genetic analysis of the clonal stability of Chinese hamster ovary cells for recombinant protein production.  Mol Biosyst.,  2016 Jan;12(1):102-9

Yang Y*, Zhang X*, Yi L, Hou Z, Chen J, Kou X, Zhao Y, Wang H, Sun XF, Jiang C, Wang Y#, Gao S#. (2016) Naïve Induced Pluripotent Stem Cells Generated From β-Thalassemia Fibroblasts Allow Efficient Gene Correction With CRISPR/Cas9.  Stem Cells Transl Med.,  2016 Jan;5(1):8-19


2015

Huang K*, Zhang X*, Shi J*, Yao M, Lin J, Li J, Liu H, Li H, Shi G, Wang Z, Zhang B, Chen J, Pan G, Jiang C, Pei D#, Yao H#. (2015) Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells.  Sci Rep. ,  2015 Dec 7;5:17691

Fu Y*, Huang C*, Xu X*, Gu H, Ye Y, Jiang C, Qiu Z, Xie X. (2015) Direct reprogramming of mouse fibroblasts into cardiomyocytes with chemical cocktails.  Cell Res. ,  2015 Sep;25(9):1013-24

Liang X*, Zhang Q*, Cattaneo P, Zhuang S, Gong X, Spann NJ, Jiang C, Cao X, Zhao X, Zhang X, Bu L, Wang G, Chen HS, Zhuang T, Yan J, Geng P, Luo L, Banerjee I, Chen Y, Glass CK, Zambon AC, Chen J, Sun Y, Evans SM. (2015) Transcription factor ISL1 is essential for pacemaker development and function.  J Clin Invest.,  2015 Aug 3;125(8):3256-68


2014

Li D, Xie K, Ding G, Li J, Chen K, Li H, Qian J, Jiang C, Fang J. (2014) Tumor resistance to anti-VEGF therapy through up-regulation of VEGF-C expression.  Cancer Lett.,  2014 Apr 28;346(1):45-52

Hu X*, Wu R*, Shehadeh LA*, Zhou Q, Jiang C, Huang X, Zhang L, Gao F, Liu X, Yu H, Webster KA#, Wang JA#. (2014) Severe hypoxia exerts parallel and cell-specific regulation of gene expression and alternative splicing in human mesenchymal stem cells.  BMC Genomics,  2014 Apr 23;15(1):303

Huang B, Jiang C, Zhang R. (2014) Epigenetics: the language of the cell?  Epigenomics,  2014 Feb;6(1):73-88


2013

Dai X*, Jiang W*, Zhang Q*, Xu L, Geng P, Zhuang S, Petrich BG, Jiang C, Peng L, Bhattacharya S, Evans SM, Sun Y#, Chen J#, Liang X#. (2013) Requirement for Integrin-linked kinase in neural crest migration and differentiation and outflow tract morphogenesis.  BMC Biol.,  2013 Oct 16;11:107

Huang K*, Jia J*, Wu C, Yao M, Li M, Jin J, Jiang C, Cai Y, Pei D, Pan G#, Yao H#. (2013) Ribosomal RNA gene transcription mediated by the master genome regulator protein CCCTC-binding Factor (CTCF) is negatively regulated by the condensin complex.  J Biol Chem.,  2013 Sep 6;288(36):26067-77

Guo X*, Liu Q*, Wang G, Zhu S, Gao L, Hong W, Chen Y, Wu M, Liu H, Jiang C, Kang J. (2013) microRNA-29b is a novel mediator of Sox2 function in the regulation of somatic cell reprogramming.  Cell Res.,  2013 Jan;23(1):142-56


2012

Bao JQ*, Li D*, Wang L, Wu JW, Hu YQ, Wang ZG, Chen Y, Cao XK, Jiang C, Yan W#, Xu C#. (2012) MicroRNA-449 and MicroRNA-34b/c Function Redundantly in Murine Testes by Targeting E2F Transcription Factor-Retinoblastoma Protein (E2F-pRb) Pathway.  Journal of Biological Chemistry,  2012 Jun 22;287(26):21686-98

Chang GS, Noegel AA, Mavrich TN, Müller R, Tomsho L, Ward E, Felder M, Jiang C, Eichinger L, Glockner G, Schuster SC, Pugh BF. (2012) Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium.  Genome Res,  2012 Jun;22(6):1098-106


2011

Venters BJ, Wachi S, Mavrich TN, Andersen BE, Jena P, Sinnamon AJ, Jain P, Rolleri NS, Jiang C, Hemeryck-Walsh C, Pugh BF. (2011) A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces.  Mol Cell,  2011 Feb 18;41(4):480-92


2010

Zhao Z*# and Jiang C. (2010) Features of Recent Codon Evolution: A Comparative Polymorphism-Fixation Study.  Journal of Biomedicine and Biotechnology,  2010:202918 doi:10.1155/2010/202918


2009

Koerber, RT, Rhee, HS, Jiang, C, Pugh, BF. (2009) Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome.  Mol Cell,  2009 Sep 24;35(6):889-902


2008

Mavrich, TN, Ioshikhes, IP, Venters, BJ, Jiang, C, Tomsho, LP, Qi, J, Schuster, SC, Albert, I, and Pugh, BF (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome.  Genome Research,  2008 Jul;18(7):1073-1083

Albert*#, I, Wachi, S, Jiang, C, Pugh, BF (2008) GeneTrack - a genomic data processing and visualization framework.  Bioinformatics,  2008 May 15;24(10):1305-6

Kuo, PH*#, Kalsi, G, Prescott, CA, Hodgkinson, CA, Goldman, D, van den Oord, EJ, Alexander, J, Jiang, C, Sullivan, PF, Patterson, DG, Walsh, D, Kendler, KS, Riley, BP. (2008) Association of ADH and ALDH Genes with Alcohol Dependence in the Irish Affected Sib Pair Study of Alcohol Dependence (IASPSAD) Sample.  Alcoholism: Clinical and Experimental Research,  2008 May;32(5):785-95

Lee, C, Li, X, Hechmer, A, Eisen, M, Biggin, MD, Venters, BJ, Jiang, C, Li, J, Pugh, BF, Gilmour, DS. (2008) NELF and GAGA factor are linked to promoter proximal pausing at many genes in Drosophila.  Mol Cell Biol,  2008 May;28(10):3290-300


2007

Zhao, Z*# and Jiang, C (2007) Methylation-Dependent Transition Rates Are Dependent on Local Sequence Lengths and Genomic Regions.  Mol Biol Evol,  2007 Jan;24(1):23-5


2006

Seo, D, Jiang, C and Zhao, Z (2006) A novel statistical method to estimate the effective SNP size in vertebrate genomes and categorized genomic regions.  BMC Genomics,  2006 Dec 29;7(1):329

Boddu, J, Jiang, C, Sangar, V, Olson, T, Peterson, T, and Chopra, S (2006) Comparative structural and functional characterization of sorghum and maize duplications containing orthologous Myb transcription regulators of 3-deoxyflavonoid biosynthesis.  Plant Molecular Biology,  2006 Jan;60(2):185-99



Book Chapter


Zhao, Z and Jiang, C (2007) Investigation of the CpG Effect in Mammalian Genomes - Chapter I in: Kobayashi TB editor.  DNA Methylation Research Trends, Pg 1-24.  Nova Science Publishers, Inc., Hauppauge, NY (ISBN 1-60021-721-4)